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"Molecular dynamic simulation is one field of science that uses computer as a resource for computational methods to calculate the number of forces acting within a molecular system and analyzing its movement. This simulation is useful for the discovery of drug compounds from an illness. This study uses Gromacs as molecular dynamics application which is running on cluster computing environment. A significant speed up is obtained during the experiments. "

"ABSTRACTOne of the processes requiring HPC environments is Molecular Dynamics ( MD ) . In tropical countries, the MD process is very important in the preparation of virtual screening experiments for anti-malaria search. Previous works on the virtual screening project for anti-malaria search conducted by WISDOM project uses grid infrastructure with 1,700 CPUs of various infrastructure provided in 15 countries [13]. In silico anti malaria compounds searching from Indonesian medical plants using virtual screening methods are urgently required. This can reduce the cost and time required compared to the direct searching or examining each compound by in vitro and in vivo which will spend a lot of time and expense . However, the use of thousands of processors is difficult for the researchers with limited resources in developing countries such as Indonesia. Our of previous studies using MD with GROMACS shows the improvement of the simulation time using Cluster. But that is not the case for some of our previous works with AMBER on Cluster where we did not obtain significant speed up. However, our previous works running GROMACS on GPUs provided significant speed up about 12 times faster than that run on Cluster. In this study , we build a GPU -based computing environment and have some MD simulation with AMBER. We used several computing environments such as cluster with 16 cores , GPU Geforce GTX 465 , GTX 470 , GTX 560 , GTX 680 , and GTX 780 . In addition to PfENR ( Plasmodium falciparum Enoyl acyl Carrier Protein Reductase ) enzyme , as benchmark we also conducted MD experiments on Myoglobin protein , Dihydrofolate reductase (DHFR) protein, and Ras - Raf protein . All experimental results showed that the slowest MD processes occurred on Cluster, followed in increasing order by GTX 560, GTX 465, GTX 470, GTX 680 and GTX 780. While the GPU speed up relative to cluster is about 24 , 26 , 32 , 24 , 77 and 101, respectively. "

"ABSTRACTMolecular Dynamics (MD) is one of processes that requires High Performance Computingenvironments to complete its jobs. In the preparation of virtual screening experiments, MD is one ofthe important processes particularly for tropical countries in searching for anti-Malaria drugs. Thesearch for anti-Malaria has previously conducted, for example by WISDOM project utilizing 1,700CPUS. This computing infrastructure will be one of the limitation for country like Indonesia that alsoneeds in silico anti malaria compounds searching from the country medical plants. Thus findingsuitable and affordable computing environment is very important. Our previous works showed that ourdedicated Cluster computing power with 16 cores performance better than those using fewer cores,however the GPU GTX family computing power is much better.In this study, we investigate further our previous experiment in finding more suitable computingenvironment on much better hardware specification of non dedicated Cluster computing and GPUTesla. We used two computing environments, the first one is Barrine HPC Cluster of The University ofQueensland which has 384 compute nodes with 3144 computing cores. The second one is Delta FutureGrid GPU Cluster which has 16 computing nodes with 192 computing cores, each nodes equippedwith 2 NVIDIA Tesla C2070 GPU (448 cores). The results show that running the experiment on adedicated computing power is much better than that on non dedicated ones, and the GPU performanceis still much better than that of Cluster."

"The invention of graphical processing units (GPUs) has significantly improved the speed of long processes used in molecular dynamics (MD) to search for drug candidates to treat diseases, such as malaria. Previous work using a single GTX GPU showed considerable improvement compared to GPUs run in a cluster environment. In the current work, AMBER and dual GTX 780 and 970 GPUs were used to run an MD simulation on the Plasmodium falciparum enoyl-acyl carrier protein reductase enzyme; the results showed that performance was improved, particularly for molecules with a large number of atoms using single GPU."

"Fiksasi biologis yang melibatkan mikroalga adalah proses kompleks yang masih belum sepenuhnya dipahami karena keterbatasan metode eksperimental saat ini yang hanya menyediakan analisis pada skala makroskopik. Dalam penelitian ini, kami menyelidiki mekanisme permeasi molekul CO2 melalui membran sel mikroalga menggunakan simulasi dinamika molekuler. Kami memodelkan membran sel mikroalga sebagai molekul DPPC (Dipalmitoylphosphatidylcholine), sebuah jenis fosfolipid yang dominan dalam membran sel makhluk hidup. Kami menggunakan model atom lengkap dengan gaya medan CHARMM (Chemistry at Harvard Macromolecular Mechanics). Semua simulasi, termasuk minimisasi, ekuilibrasi , dan pengumpulan data, dilakukan menggunakan paket perangkat lunak LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). Hasil penelitian menunjukkan bahwa molekul CO2 dapat menembus membran sel mikroalga, dengan hambatan energi tinggi pada antarmuka antara wilayah lipid dan air. Koefisien difusi molekul CO2 melalui membran sel mikroalga berkisar antara 1.81 hingga 2.69 x 10-5 cm²/s, dan permeabilitasnya berkisar antara 0.17 hingga 0.22. Variasi suhu antara 300 dan 320 K tidak menunjukkan efek signifikan pada karateristik perpindahan molekul CO2.

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Biological fixation involving microalgae is a complex process that remains poorly understood due to the limitations of current experimental methods, which only provide macroscopic analysis. In this research, we investigate the mechanism of CO2 molecule permeation through the microalgae cell membrane using molecular dynamics simulations. We model the microalgae cell membrane as DPPC (Dipalmitoylphosphatidylcholine), a dominant phospholipid in living cell membranes. We use an all-atom model with the CHARMM (Chemistry at Harvard Macromolecular Mechanics) force field. All simulations, including minimization, equilibration, and data collection, are conducted using the LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) software package. The results show that CO2 molecules can permeate through the microalgae cell membrane, encountering a high energy barrier at the interface between the lipid and water regions. The diffusion coefficient of CO2 molecules through the microalgae cell membrane ranges from 1.81 to 2.69 x 10-5 cm²/s, and the permeability ranges from 0.17 to 0.22. The temperature variation between 300 and 320 K shows no significant effect on the transport properties of CO2 molecules."

"Rem GTPase is a member ofRGK subfamily (Rad, Rem, Rem2, Gem and Kir) found recently. Rem is highly expressed at cardiac muscle.[l] Crystal structure of Rem (2NZJ) unveiled disordered structures of switch I (residue 102-110) and switch II (residue 135-145). These both regions have been acknowledged to be involved in nucleotide binding and GTP hydrolysis . The purpose of this study is to construct Rem GTPase model by using homology modeling method and to analyze the movements of Rem by performing molecular dynamics (MD) simulation. The selected Rem model, model_Rem_6.pdb, was constructed from multiple templates composed of 421P _A (Ras), 2A78_A (RalA), and 2NZJ_A. Furthermore Rem model was used for ten nanoseconds MD simulation provided for GDP, GTP and without ligand system by using GROMACS 3.3.2. The result was observed from visualization point of view, potential energy, RMSD and RMSF factors. MD simulation revealed that switch regions moved more flexible than other regions in the structure and tended to move away from nucleotide binding site, distinct from the movements of Ras switches which had shown interactions occurred within y­phosphate and both switches."